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Re: [Adun-dev] Working FFML Raul E Alcantara Wed Mar 03 10:00:33 2010

Ok so now it seems to be progressing further than before!

It now seem to calculate the forces too... there are two nonzero entries 
in the output forceMatrix for the atoms with the harmonic term.

I'll do further checks to see that the values are correct.

--Raul


Jordi Villà wrote:
> Thanks a lot, Michael,
> I think your concept solution (multiple force fields applied to the  
> same system) is the optimal. Raúl, let me know the results of your  
> tests on the RNA force field
>
> Jordi
>
> On Mar 3, 2010, at 5:17 PM, Michael Johnston wrote:
>
>   
>> Hi,
>>
>>      The ffml branch now should compile and actually work - I can run  
>> the test simulation without any errors (allthough the mathml force- 
>> field calculates no forces). To compile (first do an update)
>>
>> 1 - Compile and install the ffml library
>> 2 - Compile and install AdunKernel
>>
>> I had to add a temporary dependency on libffml to AdunKernel to get  
>> it to build - We can get rid of this later by compiling all the  
>> MathML stuff  as one "extension" bundle.
>>
>> There were  a couple of minor bugs that I've removed. The main  
>> problem was the Template. The MathML force-field was placed as a  
>> custom-term of the Charmm force-field.
>> This isn't necessary (or possible) - You can add other terms to a  
>> force-field but not another force-field.
>> What you want is two different force-fields - Charmm and MathML -  
>> operating on the same system. To do this you just have to add the  
>> force-field names to the forceFieldCollection entry.
>> I've update the Template with the changes so you can check them -  
>> its just a deletion of one-line and addition of one-other.
>>
>> Michael
>> _______________________________________________
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>>     
>
> ----
> Jordi Villà i Freixa
> CBBL at Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
> Parc de Recerca Biomèdica de Barcelona
> C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
> Tel: +34 93 316 0504 // Fax: +34 93 316 0550
> e-mail: [EMAIL PROTECTED] // http://cbbl.imim.es
>
>
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>   


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